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Detailed information for vg1219847688:

Variant ID: vg1219847688 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19847688
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, G: 0.09, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AGGAAGAAGATGACACCGAGCTCCAATCTCGCGGCACCAATCAAGGGGTTTCTTGATCCCAACATTGAGGGCAATGCATCCATTTCCCGGTGAACCAGAG[T/G]
ATGAATTCCTCAGTTCACATTTGGAACAGATAGAGGGCGTGCAGGAGAGGCTGTTTGGCGAAGCTAGGAGGTTAAAACATCAAGTCTGCCATGCGGTCTT

Reverse complement sequence

AAGACCGCATGGCAGACTTGATGTTTTAACCTCCTAGCTTCGCCAAACAGCCTCTCCTGCACGCCCTCTATCTGTTCCAAATGTGAACTGAGGAATTCAT[A/C]
CTCTGGTTCACCGGGAAATGGATGCATTGCCCTCAATGTTGGGATCAAGAAACCCCTTGATTGGTGCCGCGAGATTGGAGCTCGGTGTCATCTTCTTCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.20%	8.40%	0.40%	18.98%	NA
All Indica	2759	66.50%	0.70%	0.65%	32.11%	NA
All Japonica	1512	81.10%	18.50%	0.00%	0.46%	NA
Aus	269	69.50%	30.50%	0.00%	0.00%	NA
Indica I	595	43.20%	0.50%	2.18%	54.12%	NA
Indica II	465	95.90%	0.60%	0.00%	3.44%	NA
Indica III	913	58.80%	0.70%	0.33%	40.20%	NA
Indica Intermediate	786	75.80%	0.90%	0.25%	23.03%	NA
Temperate Japonica	767	69.60%	30.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	79.70%	19.50%	0.00%	0.83%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	81.10%	13.30%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219847688	T -> DEL	LOC_Os12g32840.1	N	frameshift_variant	Average:58.435; most accessible tissue: Callus, score: 87.227	N	N	N	N
vg1219847688	T -> G	LOC_Os12g32840.1	missense_variant ; p.Tyr10Asp; MODERATE	nonsynonymous_codon ; Y10D	Average:58.435; most accessible tissue: Callus, score: 87.227	unknown	unknown	TOLERATED	0.71

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219847688	3.12E-07	7.76E-10	Heading_date	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1219847688	NA	1.19E-09	Heading_date	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1219847688	NA	6.55E-07	mr1456_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1219847688	NA	2.13E-07	mr1780_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1219847688	7.78E-06	2.27E-08	mr1781_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251